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The Molecules of Life

The Molecules of Life. Chapter 2. Preview. Review of chemical bonds (covalent, ionic, hydrogen bonds) Small molecules important for life Water (properties, pH, buffer) Other small molecules Macromolecules Protein Lipid Polysaccharide Nucleic acid. Atoms and Elements. Atoms

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The Molecules of Life

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  1. The Molecules of Life Chapter 2

  2. Preview • Review of chemical bonds (covalent, ionic, hydrogen bonds) • Small molecules important for life • Water (properties, pH, buffer) • Other small molecules • Macromolecules • Protein • Lipid • Polysaccharide • Nucleic acid

  3. Atoms and Elements • Atoms • Basic unit of all matter • three major components • Protons • Electrons • Neutrons

  4. Atoms and Elements • Elements • Substance that consists of a single type of atom • 92 naturally occurring elements • 99% of all living matter by weight made up of four • Carbon • Hydrogen • Oxygen • Nitrogen • Phosphorus and sulfur make up additional 0.5%

  5. Atoms and Elements • Each element is identified by two numbers • Atomic number • Number of protons occupying the nucleus • In an uncharged element this also equals the number of electrons • Atomic mass • Number of protons plus the number of neutrons

  6. Atoms and Elements • Electrons of each element are arranged in orbital • Each orbital contain a certain number of electrons • Each orbital must be filled before electrons occupy the next • Orbitals farthest from the nucleus have the highest energy • most stable when the outer orbital contains the maximum number of electrons • 2, 8, 8 etc.

  7. Chemical Bonds and the Formation of Molecules • To fill outer orbitals atoms form bonds with other atoms • Bonds :sharing or the gain or loss of electrons • Molecules are formed when atoms bond together • Valence: the number of electrons that an atom must gain or lose to fill its outer orbital. • types of chemical bonds (vary in strength) • Covalent bonds • Ionic bonds • Hydrogen bonds

  8. Covalent Bonds • Formed by sharing of electrons between atoms • Strong (difficult to break) • Requires significant energy • Enzyme • can be polar or non-polar

  9. Covalent Bonds • Non-polar covalent • Equal attraction • H-H or C-H • Organic compound • C-C bond

  10. Covalent Bonds • Polar covalent • Unequal attraction • Produces a slight charge within the molecule • O-H

  11. Ionic Bonds • gaining or losing electrons • Loss and gain of electrons leads to charged atoms (ions) • Cation • Anion • Charged atoms are attracted to each other and form a bond between ions • Ionic bond

  12. Ionic Bonds • Ionic bonds are weaker than covalent bonds • Bonds dissociate in water • Important among weak forces holding biological molecules together

  13. Hydrogen Bonds • Weak bonds formed between polar molecules • Most commonly between hydrogen and oxygen or nitrogen • Hydrogen bonds occur between molecules such as water and DNA • Covalent bonds are formed within the molecules • Covalent bonds hold atoms together • Hydrogen bonds hold molecules together

  14. Hydrogen Bonds • Weakest of the biological bonds • Constantly being formed and broken at room temperature • Large numbers of hydrogen bonds can hold molecules together firmly • Important for molecule-molecule such as enzyme-substrate interaction.

  15. questions • What is atomic number? • Cation is formed by: • Lose electron • Share electron • Gain electron • Which is the strongest chemical bond? • Ionic bond • Hydrogen bond • Covalent bond

  16. Small molecules of the Cell--water • Most important molecule is water • Makes up over 70% of all living organisms by weight • Importance of water depends on it unusual bonding properties

  17. Bonding Properties of Water • Bonding properties of water • Hydrogen bonds form between water molecules

  18. Bonding Properties of Water • Water is a great solvent. • Polar nature accounts for ability • Molecules dissolved must contain charged atoms • Ions become surrounded by water • Na+ and Cl- ions no longer able to bond to each other

  19. Important Property of solution--pH • Acidity is measured as pH • Defined as concentration of H+ ions • potential Hydrogen • Measured on logarithmic scale of 0 to 14 • Neutral is pH 7 (H+ and OH- ions are equal solution) • acid • base • [H+] x [OH-]=10-14 • Buffer system: help to maintain neutral pH.

  20. Other Small Molecules in the Cell • small organic and inorganic molecules • ~ 1% of dry weight of bacteria composed of inorganic ions • Na+, K+, Mg2+, Ca2+, Fe2+, Cl-, PO43- and SO42- • Certain enzymes require positively charged ions for proper functioning • Negatively charged phosphate ions are essential in energy metabolism • Small organic molecules act as precursor metabolites • These are converted to the building blocks of macromolecules

  21. Macromolecules and Their Component Parts • Macromolecules are very large • Macro = large • Biological macromolecules are divided into four classes • Proteins • Polysaccharides (carbohydrates) • Lipids • Nucleic acids

  22. Macromolecules and Their Component Parts • All macromolecules are polymers • Poly = many • formed by joining smaller subunits together • dehydration reaction

  23. Macromolecules and Their Component Parts • Macromolecules are broken down into smaller subunits • hydrolysis

  24. questions • What is pH? • What is the function of buffer? • Macromolecules are formed by___ reaction of the subunits. hydrolysis dehydration

  25. Proteins and Their Functions • 50% of cell dry weight • Made up of amino acid subunits • Most versatile • Some responsibilities include • Catalyzing reactions • Composition and shape of certain bacterial structures • Gene regulation • Nutrient procurement

  26. Amino Acid Subunits • 20 different types of amino acids • common features for amino acids • The side chain differentiates the amino acids • Hydrophilic • Hydrophobic (contain methyl group) • Stereoisomers • L, D amino acid

  27. Peptide Bonds and Their Synthesis • peptide bonds • Formed between carboxyl group of one amino acid and the amino group of the following amino acid • Release water molecule

  28. Protein Structure • Protein function depends on the shape of the protein • Protein shape depends on the sequence of amino acids • Proteins have four structures • Primary • Secondary • Tertiary • Quaternary

  29. Protein Structure • Primary structure • Sequence of amino acids • In large part determines other protein features

  30. Protein Structure • Secondary structure • Primary structure folds into new configuration • Helical structure • Alpha (α) helix • Pleated structure • Beta (β) sheet • Results from weak bonds formed between amino acids • Certain sequences of the aa leads to distinct secondary structures

  31. Protein Structure • Tertiary structure • 3 dimensional structure • 2 major shapes • Globular • Fibrous • Becomes functional protein • Tertiary structure depends on primary structure and interaction with water. • Hydrophobic interaction • S-S bond (covalent)

  32. Protein Denaturation • Specific shape for proper function • breaking bonds within the protein disrupt structure • protein stop functioning • Denaturation can be reversible or irreversible • Environment determines reversibility • Heat • chemical

  33. Substituted Proteins • Proteins that has other kind of molecules covalently bond to side chain of amino acid. • Glycoprotein: sugar attached • Lipoprotein: lipid bond.

  34. questions • How many kinds of amino acid are there in a protein? • What is the primary structure of a protein? • What determine the shape of a protein?

  35. Carbohydrates • Carbohydrates are diverse group of molecules with various sizes • Play important roles in all organisms including • Common source of food and energy • Form part of nucleic acids • Form part of bacterial cell wall

  36. Carbohydrates • Carbohydrates contain carbon, hydrogen and oxygen in 1:2:1 ratio • CH2O • Monosaccharide • Classified by number of carbons in molecule • Most common monosaccharides • 5 and 6 carbon sugars

  37. Carbohydrates • Disaccharides • two monosaccharides joined through dehydration synthesis • Lactose and sucrose most common in nature • Glucose + galactose = lactose • Glucose + fructose = sucrose • Maltose less common • Glucose + glucose = maltose

  38. Carbohydrates • Polysaccharides • Serve different function • Cellulose most abundant organic molecule on earth • Polymer of glucose molecules • Principle constituent in plant cell wall • Glycogen is carbohydrate storage molecule of animals and some bacteria • Polymer of glucose subunits • Dextran storage molecule for carbon and energy for some bacteria • Polymer of glucose subunits

  39. Nucleic Acids • Two types of nucleic acid • DNA • Carry genetic code in all cells • RNA • Decodes sequence of DNA to produce proteins • Subunits of nucleic acids are nucleotides

  40. DNA • DNA are composed of 4 kinds of nucleotides. • Five carbon sugar • Deoxyribose • Phosphate molecule • Nitrogenous base • 4 kinds of base: A, T, G, C • DNA sequence are represented by base sequence

  41. DNA • Nucleotides joined through covalent bonding to form a DNA strand • phosphate of one nucleotide join the sugar of the adjacent nucleotide • Results in a sugar phosphate backbone • Direction 5’ to 3’

  42. DNA • double stranded helical molecule • hydrogen bonding between bases from each strand • Specific pairing between bases A-T, G-C • Bases are complementary

  43. RNA • Involved in decoding DNA • Structure is similar to DNA • Uracil replace thymine • ribose in place of deoxyribose • RNA is generally shorter • Single stranded.

  44. questions • What is the subunit of DNA? • What is the difference between DNA and RNA?

  45. Lipids • Critical component of the cell membrane • Membranes act a gatekeepers to the cell • Heterogeneous group of molecules • Made up of different subunits • Defining feature • Insoluble in water • Can be divided into two general classes • Simple lipids • Compound lipids

  46. Simple Lipids • Contain only carbon, hydrogen and oxygen • Most common are called fats • Made of glycerol and fatty acid • Triglyceride • Fatty acids bond to glycerol covalently through dehydration synthesis

  47. Simple Lipids • Steroids are also considered simple lipids • insoluble in water • Sterol (with OH in one ring) • Example: cholesterol

  48. Compound Lipids • fatty acids, glycerol and other elements • Phospholipid most important compound lipid • a phosphate and two fatty acids attached to a glycerol molecule • Amphiphilic molecule

  49. Compound Lipids • Phospholipids • Major component in lipid cell membrane • bilayer of phospholipids • orientation • a barrier to the entry and exit of cellular substances

  50. questions • What is the major component of cell membrane? • What is the defining feature of lipid?

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